Merge branch 'amusecode:main' into petar_test_collision

.gitignore

@@ -484,10 +484,15 @@ test_python_sockets_implementation
 .idea
 
 src/amuse/community/bonsai2/src
-src/amuse/community/*/version.py
-src/amuse/version.py
+doc/interactive_tutorial/_version.py
+src/amuse/test/suite/_version.py
+src/amuse/community/*/_version.py
+src/amuse/_version.py
 src/amuse/community/petar/src
 src/amuse/community/seba/src
 packages/amuse*/dist
 packages/dist
 src/amuse/community/phantom/src
+
+# standard directory for a virtualenv
+env/

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for amuse 2023.3.1.dev41+gaa14f8bf8.d20230322.
+# Generated by GNU Autoconf 2.71 for amuse 2023.7.0.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -668,8 +668,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='amuse'
 PACKAGE_TARNAME='amuse'
-PACKAGE_VERSION='2023.3.1.dev41+gaa14f8bf8.d20230322'
-PACKAGE_STRING='amuse 2023.3.1.dev41+gaa14f8bf8.d20230322'
+PACKAGE_VERSION='2023.7.0'
+PACKAGE_STRING='amuse 2023.7.0'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1505,7 +1505,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures amuse 2023.3.1.dev41+gaa14f8bf8.d20230322 to adapt to many kinds of systems.
+\`configure' configures amuse 2023.7.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1571,7 +1571,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of amuse 2023.3.1.dev41+gaa14f8bf8.d20230322:";;
+     short | recursive ) echo "Configuration of amuse 2023.7.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1725,7 +1725,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-amuse configure 2023.3.1.dev41+gaa14f8bf8.d20230322
+amuse configure 2023.7.0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -2259,7 +2259,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by amuse $as_me 2023.3.1.dev41+gaa14f8bf8.d20230322, which was
+It was created by amuse $as_me 2023.7.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -4942,13 +4942,13 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
         if test -n "$PYTHON"; then
       # If the user set $PYTHON, use it and don't search something else.
-      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether $PYTHON version is >= 3.5" >&5
-printf %s "checking whether $PYTHON version is >= 3.5... " >&6; }
+      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether $PYTHON version is >= 3.7" >&5
+printf %s "checking whether $PYTHON version is >= 3.7... " >&6; }
       prog="import sys
 # split strings by '.' and convert to numeric.  Append some zeros
 # because we need at least 4 digits for the hex conversion.
 # map returns an iterator in Python 3.0 and a list in 2.x
-minver = list(map(int, '3.5'.split('.'))) + [0, 0, 0]
+minver = list(map(int, '3.7'.split('.'))) + [0, 0, 0]
 minverhex = 0
 # xrange is not present in Python 3.0 and range returns an iterator
 for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i]
@@ -4970,8 +4970,8 @@ fi
     else
       # Otherwise, try each interpreter until we find one that satisfies
       # VERSION.
-      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for a Python interpreter with version >= 3.5" >&5
-printf %s "checking for a Python interpreter with version >= 3.5... " >&6; }
+      { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for a Python interpreter with version >= 3.7" >&5
+printf %s "checking for a Python interpreter with version >= 3.7... " >&6; }
 if test ${am_cv_pathless_PYTHON+y}
 then :
   printf %s "(cached) " >&6
@@ -4983,7 +4983,7 @@ else $as_nop
 # split strings by '.' and convert to numeric.  Append some zeros
 # because we need at least 4 digits for the hex conversion.
 # map returns an iterator in Python 3.0 and a list in 2.x
-minver = list(map(int, '3.5'.split('.'))) + [0, 0, 0]
+minver = list(map(int, '3.7'.split('.'))) + [0, 0, 0]
 minverhex = 0
 # xrange is not present in Python 3.0 and range returns an iterator
 for i in list(range(0, 4)): minverhex = (minverhex << 8) + minver[i]
@@ -7776,7 +7776,13 @@ else $as_nop
         fi
         cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
+ifelse(main, main, , # Avoid conflicting decl of main.
+    /* Override any gcc2 internal prototype to avoid an error.  */
 
+    /* We use char because int might match the return type of a gcc2
+        builtin and then its argument prototype would still apply.  */
+    char main();
+    )
 int
 main (void)
 {
@@ -7860,7 +7866,13 @@ else $as_nop
         fi
         cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
+ifelse(main, main, , # Avoid conflicting decl of main.
+    /* Override any gcc2 internal prototype to avoid an error.  */
 
+    /* We use char because int might match the return type of a gcc2
+        builtin and then its argument prototype would still apply.  */
+    char main();
+    )
 int
 main (void)
 {
@@ -14322,7 +14334,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by amuse $as_me 2023.3.1.dev41+gaa14f8bf8.d20230322, which was
+This file was extended by amuse $as_me 2023.7.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -14377,7 +14389,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-amuse config.status 2023.3.1.dev41+gaa14f8bf8.d20230322
+amuse config.status 2023.7.0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -21,7 +21,7 @@ AC_ARG_VAR([PYTHON], [Python interpreter])
 
 AC_SUBST(FC_ISO_C_BINDINGS)
 
-AM_PATH_PYTHON([3.5])
+AM_PATH_PYTHON([3.7])
 
 AC_PATH_PROG([PYTHON], [$PYTHON], [])
 AC_ARG_VAR([NVCC], [CUDA compiler command])

doc/install/howto-install-AMUSE.rst

@@ -170,3 +170,56 @@ individual codes can be build with:
     make {code}.code
 
 with {code} the name of the code in lower case. 
+
+Installation on HPC systems using modules (tested for Snellius)
+***************************************************************
+
+Note that the modules on your local HPC system may be differently named.
+
+.. code-block:: sh
+
+    module load 2022
+    module load foss/2022a
+
+Load python.
+
+.. code-block:: sh
+
+    module load Python/3.10.4-GCCcore-11.3.0 # or another version of python, 3.7 or higher
+
+
+Following AMUSE documentation (see above), download/upgrade the python package: (--user is required by Snellius)
+
+.. code-block:: sh
+
+    mkdir MY_PROJECT_DIR
+    cd MY_PROJECT_DIR
+    python3 -m venv env  # initialise a Python virtual environment, which will contain all the packages we install
+    source env/bin/activate  # activate the virtual environment - this must be repeated every time you log in
+    pip install --upgrade pip
+    cd AMUSE_DIR  # change to where you downloaded AMUSE
+    pip install -r requirements.txt --upgrade  # install/upgrade all required packages
+    pip install matplotlib  # not required but highly recommended
+    pip install -e .
+
+Now you can build the AMUSE framework with 
+
+.. code-block:: sh
+
+    make framework
+
+Finally, build AMUSE individual codes by running from the AMUSE directory:
+
+.. code-block:: sh
+
+    make {code}.code
+
+When you log in again (and in your SLURM scripts), you will need to load the same modules and activate the same environment:
+
+.. code-block:: sh
+
+    module load 2022
+    module load foss/2022a
+    module load Python/3.10.4-GCCcore-11.3.0 # or another version of python, 3.7 or higher
+    cd MY_PROJECT_DIR
+    source env/bin/activate

m4/ax_mpi.m4

@@ -80,7 +80,7 @@
 
 AU_ALIAS([ACX_MPI], [AX_MPI])
 AC_DEFUN([AX_MPI], [
-AC_PREREQ(2.50) dnl for AC_LANG_CASE
+AC_PREREQ([2.71]) dnl for AC_LANG_CASE
 
 AC_LANG_CASE([C], [
 	AC_REQUIRE([AC_PROG_CC])
@@ -194,16 +194,16 @@ if test x = x"$MPILIBS"; then
 	AC_CHECK_LIB(mpich, MPI_Init, [MPILIBS="-lmpich"])
 fi
 
-dnl We have to use AC_TRY_COMPILE and not AC_CHECK_HEADER because the
+dnl We have to use AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[]])],[],[]) and not AC_CHECK_HEADER because the
 dnl latter uses $CPP, not $CC (which may be mpicc).
 AC_LANG_CASE([C], [if test x != x"$MPILIBS"; then
 	AC_MSG_CHECKING([for mpi.h])
-	AC_TRY_COMPILE([#include <mpi.h>],[],[AC_MSG_RESULT(yes)], [MPILIBS=""
+	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <mpi.h>]], [[]])],[AC_MSG_RESULT(yes)],[MPILIBS=""
 		AC_MSG_RESULT(no)])
 fi],
 [C++], [if test x != x"$MPILIBS"; then
 	AC_MSG_CHECKING([for mpi.h])
-	AC_TRY_COMPILE([#include <mpi.h>],[],[AC_MSG_RESULT(yes)], [MPILIBS=""
+	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <mpi.h>]], [[]])],[AC_MSG_RESULT(yes)],[MPILIBS=""
 		AC_MSG_RESULT(no)])
 fi],
 [Fortran 77], [if test x != x"$MPILIBS"; then

m4/ax_openmp.m4

@@ -68,7 +68,7 @@
 #serial 8
 
 AC_DEFUN([AX_OPENMP], [
-AC_PREREQ(2.59) dnl for _AC_LANG_PREFIX
+AC_PREREQ([2.71]) dnl for _AC_LANG_PREFIX
 
 AC_CACHE_CHECK([for OpenMP flag of _AC_LANG compiler], ax_cv_[]_AC_LANG_ABBREV[]_openmp, [save[]_AC_LANG_PREFIX[]FLAGS=$[]_AC_LANG_PREFIX[]FLAGS
 ax_cv_[]_AC_LANG_ABBREV[]_openmp=unknown

m4/fftw.m4

@@ -4,7 +4,7 @@
 #
 AC_DEFUN([AX_FFTW],[
         AC_ARG_WITH(fftw,
-             AC_HELP_STRING([--with-fftw=PFX], [Prefix where FFTW has been installed] ),
+             AS_HELP_STRING([--with-fftw=PFX],[Prefix where FFTW has been installed ]),
              [
                 test "$withval" = no && AC_MSG_WARN([fftw is a required package for some modules])
                 test "$withval" = yes || fftw_prefix="$withval" 

m4/gmp.m4

@@ -4,7 +4,7 @@
 #
 AC_DEFUN([AX_GMP],[
         AC_ARG_WITH(gmp,
-             AC_HELP_STRING([--with-gmp=PFX], [Prefix where GMP has been installed] ),
+             AS_HELP_STRING([--with-gmp=PFX],[Prefix where GMP has been installed ]),
              [
                 test "$withval" = no && AC_MSG_WARN([gmp is a required package for some modules])
                 test "$withval" = yes || gmp_prefix="$withval" 

m4/gsl.m4

@@ -89,19 +89,17 @@ AC_ARG_ENABLE(gsltest, [  --disable-gsltest       Do not try to compile and run
               echo "*** Could not run GSL test program, checking why..."
               CFLAGS="$CFLAGS $GSL_FLAGS"
               LIBS="$LIBS $GSL_LIBS"
-              AC_TRY_LINK([
+              AC_LINK_IFELSE([AC_LANG_PROGRAM([[
     #include <stdio.h>
-    ],      [ return 0; ],
-            [ echo "*** The test program compiled, but did not run. This usually means"
+    ]], [[ return 0; ]])],[ echo "*** The test program compiled, but did not run. This usually means"
               echo "*** that the run-time linker is not finding GSL or finding the wrong"
               echo "*** version of GSL. If it is not finding GSL, you'll need to set your"
               echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
               echo "*** to the installed location  Also, make sure you have run ldconfig if that"
               echo "*** is required on your system"
           echo "***"
               echo "*** If you have an old version installed, it is best to remove it, although"
-              echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"],
-            [ echo "*** The test program failed to compile or link. See the file config.log for the"
+              echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"],[ echo "*** The test program failed to compile or link. See the file config.log for the"
               echo "*** exact error that occured. This usually means GSL was incorrectly installed"
               echo "*** or that you have moved GSL since it was installed. In the latter case, you"
               echo "*** may want to edit the gsl-config script: $GSL_CONFIG" ])